Epiviz File Server
Compute and Query Parser for Genomic Files
Description
Epiviz file Server is a Python library, to query genomic files, not only for visualization but also for transformation. The library provides various modules to perform various tasks - - Parser to read various genomic file formats, - Query to access only necessary bytes of file, - Compute to apply transformations on data, - Server to instantly convert the datasets into an API and - Visualization.
A quick overview of the library and its features, are described in an IPython notebook available at - https://epiviz.github.io/post/2019-02-04-epiviz-fileserver/
Note
The library requires the server hosting the data files to support HTTP range requests so that the file server’s parser module can only request the necessary byte-ranges needed to process the query
The library currently supports indexed genomic file formats like BigWig, BigBed, Bam (with bai), Sam (with sai) or any genomic data file that can be indexed using tabix.
Developer Notes
This project has been set up using PyScaffold 3.1. For details and usage information on PyScaffold see https://pyscaffold.org/.
use a virtualenv for testing & development. To setup run the following commands from the project directory
virtualenv env --python=python3
source env/bin/activate # (activate.fish if using the fish-shell)
pip install -r requirements.txt
# to deactivate virtualenv
deactivateTest - `python setup.py test`
Docs - `python setup.py docs`
- Build
source distribution `python setup.py sdist`
binary distribution `python setup.py bdist`
wheel distribution `python setup.py bdist_wheel`
1 maintainer
Metadata
1 maintainer
Release files for epivizFileServer 0.2.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| epivizFileServer-0.2.7.tar.gz | 13.4 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| epivizFileServer-0.2.7-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 13.5 MB
Release files / epivizFileServer-0.2.7.tar.gz
| Download URL | epivizFileServer-0.2.7.tar.gz |
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| Size | 13.4 MB |
| Tags | Source |
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Release files / epivizFileServer-0.2.7-py2.py3-none-any.whl
| Download URL | epivizFileServer-0.2.7-py2.py3-none-any.whl |
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| Size | 55.6 kB |
| Tags | Python 2 Python 3 |
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